MDPP Wiki

The Biozentrum Micrograph Data Processing Program (MDPP)

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AA ...... angular average
AB ...... angular back interpolation
AC ...... average contour
AD ...... angular addition
AF ...... angular forward Fourier transform
AI ...... angular interpolation
AK ...... projection stack correlate
AM ...... angular modulus
AO ...... alter output/input files
AR ...... angular reverse Fourier transform
AS ...... arbitary section
AT ...... attach a buffer file
AU ...... autocorrelation
AV ...... average, histogram of image

BD ...... binary dump
BF ...... Bessel forward transform: D(Z,k) transform
BG ...... background processing
BK ...... Brookhaven magnetic tape read program
BP ...... backprojection reconstruction
BR ...... Bessel reverse transform: D(Z,k) transform
BT ...... build transform

CF ...... compressed forward Fourier transform
CG ...... generate CGM files
CM ...... contour manipulation
CN ...... change number
CO ...... contour output
CR ...... center regression
CS ...... center search
CV ...... calculate volume and area
CW ...... cosine wave (model wave)
CY ...... cylindrical section

DC ...... 'discretize' array
DK ...... deconvolve 3-D array
DM ...... modify display colour table
DO ...... digital output numerically
DP ...... display on printer
DS ...... de-shadow 3-D image
DT ...... detach a buffer file
DV ...... display visually
DY ...... dyad axis symmetrization
DZ ...... digitize an image using the Eikonix

ED ...... edit array
EI ...... enhance image element
EL ...... extract layerline
EO ...... enter order
ER ...... erase display screen
ES ...... extract section
ET ...... extract tile

FC ...... filter center
FD ...... float down (helices)
FF ...... forward Fourier transform
FH ...... filter helix
FI ...... format interchange
FL ...... filter
FR ...... reverse Fourier transform
FS ...... find statistics
FT ...... float array
F3 ...... 3-D forward Fourier transform

GA ...... generate array (model image)
GB ...... grab an image from a TV screen.
GC ...... generate coefficients
GF ...... general filtering program
GH ...... generate helix (model image)
GI ...... general interpolation
GN ...... generate noise (model image)
GP ...... generate projection (model image)
GR ...... compute gradient of image
GS ...... generate scan
G3 ...... generate 3-d array from a stack

HE ...... requests HELP from MDPP
HI ...... histogram equalize
HR ...... helical reconstruction programs

IB ...... input buffer
IC ...... incore
IE ...... if error switch
IL ...... interpolate layerline
IN ...... integrate
IO ...... input/output
IS ...... integrate surface
IT ...... input tape
IV ...... invert image
IX ...... input external environment

JF ...... jump to flag
JI ...... correct image 'jitter'

KA ...... correspondance analysis: data preparation
KN ...... contour manipulation
KP ...... pick-point option of correspondance analysis
KR ...... alter array dimensions
KZ ...... alter job-step indicator

LB ...... library of '.BMD' files
LC ...... layerline correlation
LG ...... illuminate (light) a surface
LI ...... linear interpolation (computer "Markham")
LP ...... layerline plot/regression
LR ...... layerline transform regeneration
LS ...... layerline rescale

MB ...... manipulate binary image
MC ...... move center in polar of Fourier transform
MD ...... modulus
MM ...... maximum and minimum
MS ...... merge scan
MT ...... message to terminal (background only)
MV ...... play a movie loop
MW ...... make Wiener filter

NR ...... normalize

OB ...... output buffer
OD ...... on disc
OO ...... output order

PA ...... patch
PD ...... positive definite
PF ...... pad-float
PH ...... output to tape for photowrite
PJ ...... project 2D image onto a line with vernier sampling
PK ...... pack
PL ...... plotter package
PO ...... printer order
PP ...... pre-process (complex image rescaling)
PR ...... prepare for Fourier-Bessel transform
PS ...... plot scan
PZ ...... pause for terminal input
P3 ...... pack a 2-d array into a 3-d array
PT ...... protect file (nonfunctional?, but should bring back!)

QC ...... sequence gel
QS ...... list the contents of a stack

RD ...... read input file
RE ...... return to foreground operation
RF ...... radial filter
RH ...... read header
RN ...... rename (subtitle)
RO ...... rotate image
RS ...... restore
RV ...... replace value
RW ...... Read/Write Apollo transfer file
R3 ...... reverse 3-D Fourier transform

SA ...... stack add
SB ...... set buffer (nonfunctional?)
SC ...... search and correlate projections
SD ...... compute a surface display from a 3-d image
SE ...... symmetrize and extend projections
SF ...... surface relief reconstruction
SG ...... subtract gradient
SI ...... superimpose arrays
SL ...... slice density levels of pixels
SM ...... smear
SP ...... spool output file to printer
SQ ...... alter FFT indexing (skew diffraction pattern)
SO ...... smooth
SR ...... stack preparation ('stack ready')
SS ...... sub-array display
ST ...... statistics
SU ...... sum two pictures
SV ...... save image file
SX ...... sort array by a row
SW ...... spawn a line to the CLI
SZ ...... Generate Sixel output from an image

TA ...... transfer amplitudes
TC ...... translate center
TF ...... transfer function
TM ...... trim
TO ...... tape library and I/O (nonfunctional?)
TP ...... total power
TR ...... terminate MDPP
TS ...... transfer to curvilinear coordinates
TY ...... type
TZ ...... program test-bed command (user's own test function)

UA ...... unit-cell average
UB ...... unbend lattice
UP ...... unpack

VA ...... Vectorize array
VD ...... Visual display tool
VF ...... verify file title
VL ...... verify layerline
VP ...... video project
VS ...... vertical section
VW ...... view moving zoomed window of image or FT

WA ...... warp image
WF ...... bring window to foreground

XC ...... cross-correlation
XK ...... external command
XL ...... exact layerline extraction
XM ...... change MDPP default setup parameters
XP ...... execute procedure
XX ...... external exchange

ZI ...... 'zap' image onto the screen
ZU ...... zero unit
ZW ...... send MDPP to sleep for specified time
ZZ ...... job step reentry point after error

** ...... comment: written to output file
++ ...... comment: ignored anywhere on input
+@ ...... confirm input
+* ...... screen input re-direct: text following is a default line.
+- ...... comment: output to screen only

GENERAL

These are special commands to request specific services from MDPP or the
CLI for the machine you are using.

Control Characters:
<Cntl-B> ...... Pop up the Broadcast window.
<Cntl-C> ...... Terminate ongoing process (after all input is complete)
<Cntl-E> ...... Expand the image at the cursor
<Cntl-G> ...... Toggel the use of the graphics mouse
<Cntl-P> ...... Pause for 4 seconds
<Cntl-V> ...... View the work window
<Cntl-W> ...... Re-paint the screen
<Cntl-X> ...... Break-out Spawn
<Cntl-Y> ...... Force job termination (neatly!)
<Cntl-Z> ...... Abandon command (at a request for parameter input)

Note:: These command work with the screen management options of MDP.
Only <cntl-c> and <cntl-z> work in line-mode: in line mode <cntl-y>
causes MDP to abort rather than to shut down neatly.</cntl-y></cntl-z></cntl-c>

Control Commands:
? ...... Gets HELP for that command segment (if available)
?? ...... Gets HELP for that command.
HELP ...... Requests HELP on a command
MENU ...... Prints this file
PROC ...... invokes the procedure driver (same as 'XP')
XXXX ...... "XXXX" is any command, three letters or more, entered at
the terminal (e.g. DIR <string>, PUR <string>, DEL <string>
etc). All such lines are SPAWNED to the CLI for processing.

UTILITIES

These are standalone programs which are run to perform useful operations
for the enlighted user. HELP is available for all of them.

KERMIT ...... A terminal emulator and file transfer program.

LATTICE ...... Program to assist in the indexation of plane lattices
LZCMP ...... Compresses files: useful for on-line achiving of images.
LZDCM ...... Decompresses a file compressed with LZCMP
SCREW ...... Program to aid indexation of helices.
TAPEDIT ...... Copies tape-to-tape on two drives selecting files to copy
TAPEREAD ...... Reads an IBM tape to disc
TAPESPC ...... Positions a tape after a given number of files.
TAPEWRITE ...... Writes an unlabled tape in IBM format from files specified.
TPO ...... Scans a tape and lists the file characteristics and errors.

MDPP Wiki

The Biozentrum Micrograph Data Processing Program (MDPP)

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